posecheck-fast

Fast docking evaluation metrics: symmetry-corrected RMSD and lightweight PoseBusters filters.

Installation

uv pip install posecheck-fast

Features

• Symmetry-corrected RMSD — accounts for molecular symmetry (benzene, carboxylates, etc.)
• Fast PoseBusters filters — 4 distance/clash checks optimized for throughput (auto-uses CUDA if available)

Performance

Designed for throughput: ~0.03–0.12 ms/pose on the fast filter set (CPU/GPU depending on batch size).

Usage

from posecheck_fast import compute_all_isomorphisms, get_symmetry_rmsd_with_isomorphisms

# Symmetry-corrected RMSD
isomorphisms = compute_all_isomorphisms(rdkit_mol)
rmsd = get_symmetry_rmsd_with_isomorphisms(true_coords, pred_coords, isomorphisms)

from posecheck_fast import check_intermolecular_distance

# Fast filters: not_too_far_away, no_clashes, no_volume_clash, no_internal_clash
results = check_intermolecular_distance(
    mol_orig=rdkit_mol,
    pos_pred=pred_positions,      # (n_samples, n_atoms, 3)
    pos_cond=protein_positions,   # (n_protein_atoms, 3)
    atom_names_pred=lig_atoms,
    atom_names_cond=prot_atoms,
)

Related

• PoseBench — full benchmark suite
• PoseBusters — full 27-test validation
• spyrmsd — symmetry RMSD algorithms

License

MIT